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Povzetek: Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples. Six exogenous synthetic targets comprising of External RNA Control Consortium (ERCC) standards were measured alongside transcripts for three endogenous gene targets present in the background of human cell line RNA. The study was carried out under the auspices of the Nucleic Acids (formerly Bioanalysis) Working Group of the CCQM. It was coordinated by LGC (United Kingdom) with the support of National Institute of Standards and Technology (USA) and results were submitted from thirteen National Metrology Institutes and Designated Institutes. The majority of laboratories performed RNA measurements using RT-qPCR, with datasets also being submitted by two laboratories based on reverse transcription digital polymerase chain reaction and one laboratory using a next-generation sequencing method. In RT-qPCR analysis, the RNA copy number ratios between the two samples were quantified using either a standard curve or a relative quantification approach. In general, good agreement was observed between the reported results of ERCC RNA copy number ratio measurements. Measurements of the RNA copy number ratios for endogenous genes between the two samples were also consistent between the majority of laboratories. Some differences in the reported values and confidence intervals (‘measurement uncertainties’) were noted which may be attributable to choice of measurement method or quantification approach. This highlights the need for standardised practices for the calculation of fold change ratios and uncertainties in the area of gene expression profiling.
Ključne besede: RNA copy number ratio, RT-qPCR, gene expression, normalisation, standardisation, molecular diagnostic, transcriptomics, cancer, diagnostics, biomarker identification and validation
Objavljeno v DiRROS: 04.03.2025; Ogledov: 84; Prenosov: 35
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Povzetek: This study examines the occurrence and distribution of root-knot nematodes (RKN), Meloidogyne spp., in Serbia through an official survey conducted from 2021 to 2023. A total of 241 plant and soil samples were collected from 25 districts across two regions: Northern Serbia (Vojvodina Province) and Central Serbia. RKN infestations were detected in 23.7% of the samples. Among the 57 identified populations, 5 Meloidogyne species were recorded: M. incognita, M. hapla, M. luci, M. arenaria and M. javanica. Meloidogyne luci was reported in Serbia for the first time, marking a significant finding for nematology in the region. This study highlights the importance of implementing effective pest management strategies to mitigate the agricultural impact of RKN in Serbia.
Ključne besede: molecular identification, root-knot nematodes, nematodes, morphological identification, distribution, Serbia
Objavljeno v DiRROS: 05.02.2025; Ogledov: 155; Prenosov: 78
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Povzetek: The ability to identify and locate conspecifics depends on reliable transfer of information between emitter and receiver. For a majority of plant-dwelling insects communicating with substrate-borne vibrations, localization of a potential partner may be a difficult task due to their small body size and complex transmission properties of plants. In the present study, we used the leafhopper Scaphoideus titanus as a model to investigate duetting and mate searching associated with pair formation. Studying these insects on a natural substrate, we showed that the spatio-temporal structure of a vibrational duet and the perceived intensity of partner's signals influence the mating behaviour. Identification, localization and courtship stages were each characterized by a specific duet structure. In particular, the duet structure differed in synchronization between male and female pulses, which enables identification of the partner, while the switch between behavioural stages was associated with the male-perceived intensity of vibrational signals. This suggests that males obtain the information about their distance from the female and optimize their strategy accordingly. More broadly, our results show that even in insects smaller than 1 cm, vibrational signals provide reliable information needed to find a mating partner.
Ključne besede: mating behaviour, identification, localization, courtship, vibrational communication
Objavljeno v DiRROS: 02.08.2024; Ogledov: 489; Prenosov: 266
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Povzetek: In March 2021, unusual plant stuning, collar, and wet root rot of lettuce (Lactuca sativa L.) during the rosette stage was observed in two commercial fields in Serbia (44°58'N, 20°32'E; 44°45'N, 20°43'E). Disease incidence in the fields (≈ 0.9 ha each) was approximately 15 and 20%, respectively. Initial above-ground symptoms were yellowing and wilting of leaves, while below-ground symptoms were collar, wet root rot, and lesions becoming necrotic. Eventually, whole plants wilted, collapsed, and died. A total of 35 symptomatic plants were collected from the fields, and diseased tissues were cut into small pieces, surface sterilized, and plated on potato dextrose agar (PDA). Isolation resulted in 20 morphologically uniform monoconidial isolates. The isolates formed white to creamy colonies, gradually becoming salmon pink, slimy, or moist in appearance, with sparse aerial mycelia. Numerous hyphal coils with conidiophores and hyaline, smooth-surfaced, ellipsoid to ovoid, septate or aseptate conidia were formed (4.5 to 10.1×1.2 to 3.7 μm (n = 100)). To confirm the species identity, the internal transcribed spacer (ITS) region and the D1/D2 region of a selected representative isolate 13-3-c were amplified and sequenced by using primer pairs ITS1/ITS4 (White et al. 1990) and N1/N2 (O’Donnell and Gray 1995), respectively. The sequences were deposited in GenBank (ITS: OR880564 and D1/D2: OR880567). Sequence analysis revealed 100% nucleotide identity with P. cucumerina isolates from different countries deposited in the NCBI GenBank, including isolate MH860704 (Vu et al. 2019) (ITS region) and isolate KY662256 (Su et al. 2017) (D1/D2 region). Neighbor-joining analysis was conducted based on the combined ITS and D1/D2 regions, and the tree was constructed with the substitution models (1,000 bootstrap). The combined phylogeny confirmed that the sequences shared a common clade with P. cucumerina. Hence, morphological, microscopic, and molecular characterization confirmed the pathogen as P. cucumerina (Palm et al., 1995; Carlucci et al., 2012). In a pathogenicity assay, 10 isolates were tested. Five 30-day-old lettuce plants (cv. Majska Kraljica) per isolate were root-dipped in the conidial suspensions (1×105 conidia/ml). The 10 inoculated plants were transplanted into 1 L pots containing sterile substrate (Floragard, Germany). Plants treated with sterile distilled water were used as controls. Plants were maintained in a greenhouse at 25 to 28°C under a 12-hour photoperiod (Cai et al., 2021). Four weeks after inoculation, stunting, chlorosis, and wilting of plants were observed, while collars and roots exhibited typical decaying symptoms. No symptoms were observed on the control plants. The pathogen was reisolated from symptomatic tissue as previously described. Koch's postulates were completed by confirming the identity of reisolates based on morphological features. To our knowledge, this is the first report of P. cucumerina on lettuce or any other crop in Serbia. P. cucumerina is already known as a pathogen of lettuce and other hosts grown in many countries worldwide, as well as in some European countries (Belgium, England, Italy, the Netherlands, and Switzerland) (Zhang et al. 2019). This emerging pathogen may cause significant economic losses in lettuce production in Serbia and in the entire Balkan region. Our results may help to develop effective management strategies based on accurate and timely identification and regular pathogen monitoring.
Ključne besede: detection, identification, salat, plant diseases
Objavljeno v DiRROS: 17.05.2024; Ogledov: 507; Prenosov: 238
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Povzetek: Aerosol vertical profiles are valuable inputs for the evaluation of aerosol transport models, in order to improve the understanding of aerosol pollution ventilation processes which drive the dispersion of pollutants in mountainous regions. With the aim of providing high-accuracy vertical distributions of particle mass concentration for the study of aerosol dispersion in small-scale valleys, vertical profiles of aerosol mass concentration for aerosols from different sources (including Saharan dust and local biomass burning events) were investigated over the Vipava valley, Slovenia, a representative hot-spot for complex mixtures of different aerosol types of both anthropogenic and natural origin. The analysis was based on datasets taken between 1–30 April 2016. In-situ measurements of aerosol size, absorption, and mass concentration were combined with lidar remote sensing, where vertical profiles of aerosol concentration were retrieved. Aerosol samples were characterized by SEM-EDX, to obtain aerosol morphology and chemical composition. Two cases with expected dominant presence of different specific aerosol types (mineral dust and biomass-burning aerosols) show significantly different aerosol properties and distributions within the valley. In the mineral dust case, we observed a decrease of the elevated aerosol layer height and subsequent spreading of mineral dust within the valley, while in the biomass-burning case we observed the lifting of aerosols above the planetary boundary layer (PBL). All uncertainties of size and assumed optical properties, combined, amount to the total uncertainty of aerosol mass concentrations below 30% within the valley. We have also identified the most indicative in-situ parameters for identification of aerosol type.
Ključne besede: valley air pollution, aerosol vertical distributions, lidar remote sensing, in-situ measurements, aerosol identification
Objavljeno v DiRROS: 03.03.2022; Ogledov: 1437; Prenosov: 522
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